feat: clinical infrastructure for blood biomarker clocks#203
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marcbal77 wants to merge 1 commit intobio-learn:masterfrom
Open
feat: clinical infrastructure for blood biomarker clocks#203marcbal77 wants to merge 1 commit intobio-learn:masterfrom
marcbal77 wants to merge 1 commit intobio-learn:masterfrom
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Add GeoData clinical layer, biomarker registry with unit conversions, required_features() interface on all models, and NHANES-to-GeoData bridge. Foundation for clinical aging clocks (PhenoAge, KDM, Bortz, etc.) Addresses bio-learn#194
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Summary
clinicaldata layer toGeoData(5th layer alongside dnam, rna, protein_alamar, protein_olink)GeoData.from_clinical_matrix(df, source_units=, units=)factory for loading clinical blood test databiolearn.clinical.registry) with canonical names, units, valid ranges, and unit conversions for 16 biomarkersrequired_features()method to all 12 model classes, returning{"layer": str, "features": list, "metadata": list}load_nhanes_as_geodata()bridge function inbiolearn.loadThis is PR 1 of the clinical clocks initiative. It ships only infrastructure (no clock implementations). All 69 existing clocks continue to work unchanged. Foundation for PhenoAge Clinical, KDM, Bortz Blood Age, and other clinical aging clocks in subsequent PRs.
Partial fix for #194.
1.0 API surfaces for review
These interfaces will become stable at 1.0.0. Please review carefully:
GeoData.from_clinical_matrix(df, source_units=, units=)signaturemodel.required_features()return format{"layer": str, "features": list, "metadata": list}GeoData.clinicalattribute (features-as-rows, samples-as-columns)BIOMARKER_REGISTRYstructureTest plan
required_features()interface test across all 69 modelsrequired_features()matchesmethylation_sites()for dnam modelsmake formatclean